[gmx-users] calculation of distance between the center of geometry of two proteins

[Mark Abraham]

Hi,

g_dist does not take selection arguments so you cannot use -select or
anything that was an argument to it. You can either rely on the default
selections that all GROMACS tools make if there is no index file, or use
e.g. g_select to make an index file with the selections you want.

Note that gmx distance in more recent versions of GROMACS has the -select
keyword, which you should probably install and use :-)

Mark

On Mon, May 28, 2018, 11:55 SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> after deleting -select
> this error is coming
> Invalid command line argument:
> cog of group "Chain_A" plus cog of group "Chain_B"
>
>
> On 5/28/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> > Delete from -select.. previous are ok
> >
> > On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, <islamshahee at gmail.com>
> wrote:
> >
> >> hi,
> >> to calculate the distance between the center of geometry of two
> >> proteins, i am using this command
> >> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> >> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> >> Invalid command line argument:
> >> -select
> >> here in this index file the two chain group name Chain_A and Chain_B
> >> how i will select the two chain.
> >>
> >> thanking you
> >> shahee islam
> >> university of calcutta
> >> --
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